Tensions have once again flared between Indonesia and Australia over asylum seeker policy after a boat that was pushed back from Christmas Island by the Royal Australian Navy ran out of fuel off Indonesia.

On Thursday evening - just hours before a two-day summit on refugees began in Jakarta with 14 countries participating including Australia - the boat carrying 16 asylum seekers and an Indonesian captain washed up at a beach in West Kupang.

The male asylum seekers, who are from India, Nepal and Bangladesh, at Nusa Tenggara Timur police station.

The Indonesian Foreign Ministry on Friday reiterated its opposition to Australia's boat push-back policy, which it says puts lives at risk and is not a sustainable solution.

An Australian Navy vessel approaches a suspected refugee boat off the coast of Christmas Island last week.

"Unilateral action is not in line with our spirit of co-operation," Vice Minister for Foreign Affairs Muhammad Fachir said outside the meeting.

"Those who were sent back - what about their fate? It should become our common concern."

Mr Fachir said the latest boat incident would not disturb the refugee round table, which would focus on the root causes of the irregular movements of persons. However Indonesia will seek an explanation from the Australian government.

Australia is being represented at the round table by the ambassador for people smuggling issues for Australia, Andrew Goledzinowski, who will chair a panel on Saturday on future co-operation among affected countries.

"The irregular migrant issue must be addressed comprehensively, it cannot be solved by only one party such as the destination country or source country."

Mr Nasir said the Bali process was the mechanism in the region to discuss asylum seekers.

"So if we want to have a sustainable solution we have to go beyond our own self interest," he said.

One of the police officers who assisted the 16 male asylum seekers off their boat, Farah, at Tablolong beach told Fairfax Media they could have died if no one had found them.

"They were in OK condition, they were given enough food and plenty of water, but they ran out of fuel. They could've died if they sunk or if no one found them," he said.

The asylum seekers, who are from India, Nepal and Bangladesh, say they reached Christmas Island but were turned back by the Royal Australian Navy after being detained for five days.

Bangladeshi man Muhammad Anwar, 22, told Fairfax Media their vessel was leaking water so they were transferred to another boat.

"I don't know about Australia turning back boats before. The agent said Australia is good now, they take immigrants now."

Mr Anwar said he paid a people smuggling agent $USD5000 ($AUD6890) to take him to Australia.

"In my country there are many problems, everything is expensive, wages low, many killings. All I want in Australia is to make a living, and they didn't help," Mr Anwar said.

The Director-General for Multilateral Affairs at Indonesia's Ministry of Foreign Affairs, Hasan Kleib, said there was a principle of protection at sea and a code of disembarkation at a safe place.

"So this is what we would like to see as well when they are already in the middle of high seas with the unseaworthy boat… It must be better to disembark at a safety place and then deal with them (the asylum seekers) afterwards."

However he said he did not wish this incident to become a stumbling block for co-operation between the two countries.